X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fbiojava%2Fdasobert%2Fdas%2FDAS_Feature_Handler.java;h=b6badc7f37e85bcdeebdece738f71564b4553b28;hb=3d54cb06f65ea70832b8795fdefc466f26154ac5;hp=b506c513377e4902e84c49fddc13a5a197d8f465;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
index b506c51..b6badc7 100755
--- a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -30,27 +30,42 @@ import org.xml.sax.helpers.*;
 
 /**
  * a class to parse the response of a DAS - Feature request
- * @author Andreas Prlic
- *
+ * 
+ * @author Andreas Prlic Adapted for jalview use.
+ * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
+ * @author Jim Procter
+ * 
  */
-public class DAS_Feature_Handler
-    extends DefaultHandler
+public class DAS_Feature_Handler extends DefaultHandler
 {
 
   /**
-   *
+   * 
    */
   List features;
+
   boolean first_flag;
+
   HashMap feature;
+
   String featurefield;
-  String characterdata;
+
+  StringBuffer characterdata;
+
   String dasCommand;
 
   int comeBackLater;
 
   int maxFeatures;
 
+  String segmentId;
+
+  String version;
+
+  String type_id;
+
+  String type_category;
+
   public DAS_Feature_Handler()
   {
     super();
@@ -58,16 +73,51 @@ public class DAS_Feature_Handler
     features = new ArrayList();
     first_flag = true;
     featurefield = "";
-    characterdata = "";
+    characterdata = new StringBuffer();
     dasCommand = "";
     comeBackLater = -1;
     maxFeatures = -1;
+    segmentId = "";
+    version = "";
+    type_id = "";
+    type_category = "";
   }
 
-  /** specifies a maximum number of features to be downloaded. if a
-    server returns more, they will be ignored.  default is to load
-    all features
-       @param max the maximium number of features to be downloaded
+  /**
+   * get the id information specified int the SEGMENT field of the DAS response
+   * 
+   * @return the segmentId or an emtpy string if not available
+   */
+  public String getSegmentId()
+  {
+    return segmentId;
+  }
+
+  /**
+   * get the version informationspecified in the SEGMENT field of the DAS
+   * response
+   * 
+   * @return the version information of an empty string if not available
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  public boolean isMD5Checksum()
+  {
+
+    if ((version != null) && (version.length() == 32))
+      return true;
+    return false;
+  }
+
+  /**
+   * specifies a maximum number of features to be downloaded. if a server
+   * returns more, they will be ignored. default is to load all features
+   * 
+   * @param max
+   *                the maximium number of features to be downloaded
    */
 
   public void setMaxFeatures(int max)
@@ -103,52 +153,74 @@ public class DAS_Feature_Handler
   void start_feature(String uri, String name, String qName, Attributes atts)
   {
 
-    if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+    if ((maxFeatures > 0) && (features.size() > maxFeatures))
     {
-      characterdata = "";
+      characterdata = new StringBuffer();
       return;
     }
     feature = new HashMap();
     String id = atts.getValue("id");
     feature.put("id", id);
     feature.put("dassource", dasCommand);
-    characterdata = "";
+    characterdata = new StringBuffer();
   }
 
   void add_featuredata(String uri, String name, String qName)
   {
-    //System.out.println("featurefield "+featurefield+ " data "+characterdata);
+    // System.out.println("featurefield "+featurefield+ " data "+characterdata);
     // NOTE can have multiple lines ..
 
-    if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+    if ((maxFeatures > 0) && (features.size() > maxFeatures))
     {
       return;
     }
 
     String data = (String) feature.get(featurefield);
+    String featureText = characterdata.toString();
     if (data != null)
     {
-      characterdata = data + " " + characterdata;
+      featureText = data + " " + featureText;
     }
 
-    feature.put(featurefield, characterdata);
+    if (qName.equals("TYPE"))
+    {
+      if (featureText.length() < 1)
+        featureText = type_id;
+
+      feature.put("TYPE_ID", type_id);
+      feature.put("TYPE_CATEGORY", type_category);
+      type_id = "";
+      type_category = "";
+    }
+
+    feature.put(featurefield, featureText);
     featurefield = "";
-    characterdata = "";
+    characterdata = new StringBuffer();
   }
 
-  private void addLink(String uri, String name, String qName, Attributes atts)
+  private void addLink(String uri, String name, String qName,
+          Attributes atts)
   {
     String href = atts.getValue("href");
     feature.put("LINK", href);
-    characterdata = "";
+    characterdata = new StringBuffer();
     featurefield = "LINK-TEXT";
 
   }
 
+  private void addGroup(String uri, String name, String qName,
+          Attributes atts)
+  {
+    String id = atts.getValue("id");
+    feature.put("GROUP", id);
+    characterdata = new StringBuffer();
+    featurefield = "GROUP";
+  }
+
   public void startElement(String uri, String name, String qName,
-                           Attributes atts)
+          Attributes atts)
   {
-    //System.out.println("new element "+qName);
+    // System.out.println("new element "+qName);
 
     if (qName.equals("FEATURE"))
     {
@@ -158,17 +230,33 @@ public class DAS_Feature_Handler
     {
       addLink(uri, name, qName, atts);
     }
-    else if (qName.equals("METHOD") ||
-             qName.equals("TYPE") ||
-             qName.equals("START") ||
-             qName.equals("END") ||
-             qName.equals("NOTE") ||
-             qName.equals("SCORE")
-        )
+    else if (qName.equals("GROUP"))
+    {
+      addGroup(uri, name, qName, atts);
+    }
+    else if (qName.equals("METHOD") || qName.equals("TYPE")
+            || qName.equals("START") || qName.equals("END")
+            || qName.equals("NOTE") || qName.equals("SCORE")
+            || qName.equals("ORIENTATION"))
     {
-      characterdata = "";
+      characterdata = new StringBuffer();
       featurefield = qName;
     }
+    else if (qName.equals("SEGMENT"))
+    {
+      String id = atts.getValue("id");
+      if (id != null)
+        segmentId = id;
+      String v = atts.getValue("version");
+      if (v != null)
+        version = v;
+
+    }
+    if (qName.equals("TYPE"))
+    {
+      type_id = atts.getValue("id");
+      type_category = atts.getValue("category");
+    }
 
   }
 
@@ -183,14 +271,11 @@ public class DAS_Feature_Handler
   public void endElement(String uri, String name, String qName)
   {
 
-    if (qName.equals("METHOD") ||
-        qName.equals("TYPE") ||
-        qName.equals("START") ||
-        qName.equals("END") ||
-        qName.equals("NOTE") ||
-        qName.equals("LINK") ||
-        qName.equals("SCORE")
-        )
+    if (qName.equals("METHOD") || qName.equals("TYPE")
+            || qName.equals("START") || qName.equals("END")
+            || qName.equals("NOTE") || qName.equals("LINK")
+            || qName.equals("SCORE") || qName.equals("ORIENTATION")
+            || qName.equals("GROUP"))
     {
       add_featuredata(uri, name, qName);
     }
@@ -214,11 +299,14 @@ public class DAS_Feature_Handler
 
   public void characters(char ch[], int start, int length)
   {
+    if (maxFeatures > 0)
+      if (features.size() > maxFeatures)
+        return;
 
     for (int i = start; i < start + length; i++)
     {
 
-      characterdata += ch[i];
+      characterdata.append(ch[i]);
     }
 
   }